view data_manager/homer_genome_preparse.py @ 3:679673fbf0b4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit 096286097ed5cdf189a1b68c3fc34d10f4142e54

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−#!/usr/bin/env python
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−# Dan Blankenberg for bowtie2
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−# Modified by Lucille Delisle for homer
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−from __future__ import print_function
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−
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−import json
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−import optparse
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−import os
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−import subprocess
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−import sys
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−
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−DEFAULT_DATA_TABLE_NAME = "homer_preparse"
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−
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−
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−def get_id_name(params, dbkey, fasta_description=None):
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−    # TODO: ensure sequence_id is unique and does not already appear in location file
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−    sequence_id = params['param_dict']['sequence_id']
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−    if not sequence_id:
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−        sequence_id = dbkey
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−
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−    sequence_name = params['param_dict']['sequence_name']
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−    if not sequence_name:
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−        sequence_name = fasta_description
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−        if not sequence_name:
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−            sequence_name = dbkey
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−    return sequence_id, sequence_name
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−
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−
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−def homer_preparse(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id,
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−                   sequence_name, size, mask, version,
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−                   data_table_name=DEFAULT_DATA_TABLE_NAME):
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−    args = ['preparseGenome.pl', fasta_filename, '-size', str(size), '-preparsedDir', target_directory]
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−    if mask:
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−        args.append('-mask')
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−    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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−    return_code = proc.wait()
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−    if return_code:
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−        print("Error preparsing genome.", file=sys.stderr)
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−        sys.exit(return_code)
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−    mask_suffix = 'r' if mask else ''
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−    mask_suffix_name = ' masked' if mask else ''
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−    data_table_entry = dict(value=sequence_id + mask_suffix + '_' + str(size), dbkey=dbkey,
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−                            mask=str(mask), size=str(size), name=sequence_name + mask_suffix_name + ' (' + str(size) + 'bp)',
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−                            path=sequence_id + mask_suffix + '_' + str(size),
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−                            path_fasta=fasta_filename,
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−                            version=version)
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−    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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−
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−
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−def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
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−    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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−    data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
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−    data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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−    return data_manager_dict
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−
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−
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−def main():
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−    parser = optparse.OptionParser()
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−    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
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−    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
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−    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
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−    parser.add_option('-s', '--size', dest='size', action='store', type="int", default=200, help='fragment size')
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−    parser.add_option('-m', '--mask', dest='mask', action='store_true', default=False, help='mask the lower case bases (repeats)')
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−    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
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−    parser.add_option('--index_version', dest='index_version', action='store', type="string", default=None, help='index version')
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−    (options, args) = parser.parse_args()
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−
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−    filename = args[0]
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−
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−    with open(filename) as fh:
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−        params = json.load(fh)
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−    target_directory = params['output_data'][0]['extra_files_path']
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−    os.mkdir(target_directory)
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−    data_manager_dict = {}
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−
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−    dbkey = options.fasta_dbkey
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−
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−    if dbkey in [None, '', '?']:
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−        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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−
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−    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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−
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−    # preparse the genome
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−    homer_preparse(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
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−                   sequence_name, options.size, options.mask, options.index_version,
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−                   data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)
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−
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−    # save info to json file
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−    with open(filename, 'w') as fh:
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−        json.dump(data_manager_dict, fh, sort_keys=True)
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−
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−
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−if __name__ == "__main__":
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−    main()